Previous work on antigen receptor gene rearrangement (V(D)J recombination) has described the signal sequences that are recognized and the recombined products, but there was no information about the progress of the reaction. It has now become possible to detect broken DNA molecules that may be intermediates in this recombination. In the thymus of young mice, where the T cell receptor delta locus (TCRdelta) is being actively rearranged, double-strand breaks at the Ddelta2 and Jdelta1 loci are readily detected by Southern blotting. About 2% of the DNA's is broken - this is a remarkably high proportion. Broken molecules are found only in thymus and not in other tissues where TCRdelta is not undergoing rearrangement. Of the two different ends that should be generated by each break, only one (the signal end) could be detected. The coding ends may be joined more rapidly. These results provide the first direct support for a breakage - reunion model of V(D)J recombination. In related work, a physical assay has been developed that allows the direct detection of V(D)J joining in plasmid substrates, without the need for a biological enrichment.